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Not sure if there's a "best" one. I personally use Arch Linux. It's a "rolling release" distro and always gets the latest Linux kernels and software. And you can set it up the way you like, starting from a command prompt. That's probably the best thing we can do: create a minimal install and watch for any changes in eye comfort after every software addition or updates.
In your case I believe I read you use NVIDIA's proprietary driver. Did you test the open source driver, nouveau, too? It's included in the kernel and will be used automatically via modesetting when the proprietary driver is not installed/uninstalled. It might not work well on the latest cards though.
I always had a little more eye strain on Linux than on Windows (XP, 7, and 10 pre-anniversary), using the very same hardware setups.
I'd install a minimal Linux distribution + Xorg server, and maybe a small desktop environment like Xfce or even something smaller like a pure window manager without any of the "big" distros' additions like 3D desktops/compositors or other stuff that only adds complexity and makes it more difficult to narrow down sources of eye strain.
Keep in mind that latest changes in open source graphics drivers require latest kernels. In the case of NVIDIA cards, Xorg can currently be run with either the pure kernel modesetting driver (no actions required in Arch) or something on top of that like xf86-video-nouveau (a package that has to be installed separately in Arch).
I'm not familiar with AMD cards, but it should be similar there.